fastqscreen

tasks/fastqscreen.wdl

@@ -3,8 +3,8 @@ task fastq_screen {
 	File read2
 	File screen_ref_dir
 	File fastq_screen_conf
-	String read1name = basename(read1,"\\.(fastq|fq)\\.gz$")
-	String read2name = basename(read2,"\\.(fastq|fq)\\.gz$")
+	String read1name = basename(read1,".fastq.gz")
+	String read2name = basename(read2,".fastq.gz")
 	String docker
 	String cluster_config
 	String disk_size

tasks/split_gvcf_files.wdl

@@ -27,29 +27,29 @@ task split_gvcf_files {
 		do
 			mv $a $b.splited.vcf
 			if [[ $b.vcf =~ "LCL5_1" ]];then
-				cp $b.vcf ${project}.LCL5_1.vcf
+				cp $b.splited.vcf ${project}.LCL5_1.vcf
 		    elif [[ $b.vcf =~ "LCL5_2" ]]; then
-		    	cp $b.vcf ${project}.LCL5_2.vcf
+		    	cp $b.splited.vcf ${project}.LCL5_2.vcf
 	        elif [[ $b.vcf =~ "LCL5_3" ]]; then
-	        	cp $b.vcf ${project}.LCL5_3.vcf
+	        	cp $b.splited.vcf ${project}.LCL5_3.vcf
 		    elif [[ $b.vcf =~ "LCL6_1" ]]; then
-				cp $b.vcf ${project}.LCL6_1.vcf
+				cp $b.splited.vcf ${project}.LCL6_1.vcf
 		    elif [[ $b.vcf =~ "LCL6_2" ]]; then
-				cp $b.vcf ${project}.LCL6_2.vcf
+				cp $b.splited.vcf ${project}.LCL6_2.vcf
 		    elif [[ $b.vcf =~ "LCL6_3" ]]; then
-				cp $b.vcf ${project}.LCL6_3.vcf
+				cp $b.splited.vcf ${project}.LCL6_3.vcf
 		    elif [[ $b.vcf =~ "LCL7_1" ]]; then
-				cp $b.vcf ${project}.LCL7_1.vcf
+				cp $b.splited.vcf ${project}.LCL7_1.vcf
 		    elif [[ $b.vcf =~ "LCL7_2" ]]; then
-				cp $b.vcf ${project}.LCL7_2.vcf
+				cp $b.splited.vcf ${project}.LCL7_2.vcf
 		    elif [[ $b.vcf =~ "LCL7_3" ]]; then
-				cp $b.vcf ${project}.LCL7_3.vcf
+				cp $b.splited.vcf ${project}.LCL7_3.vcf
 		    elif [[ $b.vcf =~ "LCL8_1" ]]; then
-				cp $b.vcf ${project}.LCL8_1.vcf
+				cp $b.splited.vcf ${project}.LCL8_1.vcf
 		    elif [[ $b.vcf =~ "LCL8_2" ]]; then
-				cp $b.vcf ${project}.LCL8_2.vcf
+				cp $b.splited.vcf ${project}.LCL8_2.vcf
 		    elif [[ $b.vcf =~ "LCL8_3" ]]; then
-				cp $b.vcf ${project}.LCL8_3.vcf
+				cp $b.splited.vcf ${project}.LCL8_3.vcf
 	        fi
 		done